plot_features_network function

Plot features network

plot_features_network(
  ko_stat,
  map_id = "map00780",
  near_pathway = FALSE,
  modulelist = NULL,
  kos_color = c(Depleted = "seagreen", Enriched = "orange", None = "grey", Significant =
    "red2", Pathway = "#80b1d3"),
  pathway_label = TRUE,
  kos_label = TRUE,
  pathway_description = FALSE,
  kos_description = FALSE,
  str_width = 50,
  mark_module = FALSE,
  mark_color = NULL,
  return_net = FALSE,
  ...
)

Arguments

• ko_stat: ko_stat result from pvalue2zs or result of get_reporter_score
• map_id: the pathway or module id
• near_pathway: show the near_pathway if any features exist.
• modulelist: NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the KOlist as example, use custom_modulelist.
• kos_color: default, c("Depleted"="seagreen","Enriched"="orange","None"="grey","Significant"="red2")
• pathway_label: show pathway_label?
• kos_label: show kos_label?
• pathway_description: show the pathway description?
• kos_description: show the kos description?
• str_width: str width
• mark_module: mark the modules?
• mark_color: mark colors, default, c("Depleted"="seagreen","Enriched"="orange","None"="grey","Significant"="red2")
• return_net: return the network
• ...: additional arguments for c_net_plot

Returns

network plot

Examples

if (requireNamespace("MetaNet")) {
  data("reporter_score_res")
  plot_features_network(reporter_score_res, map_id = "map05230")
  plot_features_network(reporter_score_res, map_id = "map00780", near_pathway = TRUE)
}